Purdue University

Description

ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.

Available Versions

Commands - cds_with_upstream_support.py - combine_gff_records.pl - count_cds_overlaps.py - flag_top_proteins.py - gff_from_region_to_contig.pl - make_chains.py - nucseq_for_selected_genes.pl - print_high_confidence.py - print_longest_isoform.py - proteins_from_gtf.pl - prothint.py - prothint2augustus.py - run_spliced_alignment.pl - run_spliced_alignment_pbs.pl - select_best_proteins.py - select_for_next_iteration.py - spalnBatch.sh - spaln_to_gff.py

Academic license      

ProtHint depends on GenMark. To use GeneMark, users need to download license files by yourself.

Go to the GeneMark web site: http://exon.gatech.edu/GeneMark/license_download.cgi. Check the boxes for GeneMark-ES/ET/EP ver 4.69_lic and LINUX 64 next to it, fill out the form, then click "I agree". In the next page, right click and copy the link addresses for 64 bit licenss. Paste the link addresses in the commands below:

cd $HOME
wget "replace with license URL"
zcat gm_key_64.gz > .gm_key

module load biocontainers
module load prothint 

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=prothint
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers prothint  
 
prothint.py --threads 4 input/genome.fasta input/proteins.fasta --geneSeeds input/genemark.gtf --workdir test